The goal of this project is to discover lead compounds acting specifically against Helicobacter pylori, the causative agent of peptic ulcer and gastric carcinoma. Roughly every other person carries the pathogen, and there are an estimated 1.5 million cases annually of active infection in the US. The currently-used triple therapy is a combination of a proton pump inhibitor and broad spectrum antimicrobials, usually amoxicillin and clarithromycin. Increased incidence of resistance combined with poor tolerance of the regimen in some patients results in 15-25% of treatment failure. An estimated 70% of patients who fail triple therapy develop antibiotic resistance. Considering the total number of cases, treatment failure is very high, and there is an urgent need for novel classes of antimicrobials to combat this important disease. However, the last class of antibiotics acting against Gram negative species, the fluoroquinolones, was discovered 50 years ago. Apart from the core essential genome, bacteria possess hundreds of essential, species-specific genes. We hypothesize that this will provide a high likelihood for discovering species-specific antimicrobials in a conventional compound library, if we do not require hits to have broad-spectrum activity. The common focus on broad-spectrum compounds is dictated by the need to treat diseases with uncertain causes. However, peptic ulcer is caused by a single pathogen and the estimated US market for treatment is over 6 billion dollars according to the CDC. H. pylori is fastidious, and its growth is unreliable. This has prevented the development of a whole cell based HTS to identify compounds with direct activity against the pathogen until now. Our preliminary studies show that a reliable HTS against H. pylori has been developed. The screen identified several hit series which were validated for potency, novelty, low cytotoxicity and SAR, making them suitable for further development. Importantly, these compounds are specific for H. pylori since they were counter-screened against a panel of gut commensals and those with broad activity were eliminated. Specific anti-H. pylori molecules likely hit a target absent in humans, and will not harm the intestinal flora, avoiding many of the common side effects of broad spectrum antibiotics such as nausea and diarrhea. This provides preliminary validation for the approach to develop specific therapeutics targeting H. pylori. In this project, custom synthetic libraries will be produced based on four validated lead series. Detailed in vitro validation of compounds will include potency, spectrum of activity, resistance development, cytotoxicity, absorption, metabolic stability and plasma binding studies. This will ensure that a clear SAR with respect to potency is observed and that subsequent optimization for safety and pharmacokinetics is attainable. Next, compounds will undergo in vivo validation for toxicity, blood serum bioavailability and efficacy in a mouse model of H. pylori infection. Mechanism of action studies will be initiated for leads that exhibit animal efficacy. The end result of Phase I will be advanced leads that will be developed in Phase II, resulting in an IND. PUBLIC HEALTH RELEVANCE: The aim of this Phase I project is to identify compounds to treat Helicobacter pylori infection. H. pylori causes acid reflux, ulcers and stomach cancer. However, currently available therapeutics are broad spectrum antibiotics, which cause high levels of resistance and unwanted side-effects. We will develop an antibiotic that specifically targets H. pylori.